How can I constrain metal ions while running MD?

You can add zero-order bond constraints to the system. Simply add bonds between each coordinating atom and the metal ion, and then decrement the bond order to zero. This will add bond and angle constraints. It will also smear some of the charge between the coordinating atoms at the metal. The Protein Prep Wizard will do this by default for Zn atoms and others (sometimes for Ca).

Keywords: Desmond, MD, metal constraints, Ca, Zn

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